LCT: LCT data set

Description Usage Format Source References Examples

Description

These data have been extracted from the 1000 Genomes data. The data set contains the genotype matrix LCT.gen, the pedigree matrix LCT.fam and a matrix LCT.bim, corresponding to 503 individuals of European populations and 607 SNPs on chromosome 2, on a ~300kb segment containing the Lactase gene. There is also a factor LCT.pop, which gives the population from which each individual is drawn (CEU = Utah residents of Northern Western European ancestry, FIN = Finnish, GBR = England and Scottland, IBS = Iberian, TSI = Toscani).

Note that rs4988235, which associated with lactase persistence / lactose intolerence.

Usage

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Format

There are three data objects in the dataset:

LCT.gen

Genotype matrix

LCT.fam

Data frame containing all variables corresponding to a .fam file

LCT.bim

Data frame containing all variables corresponding to a .bim file

LCT.pop

Factor giving the population from which each individual is drawn

Source

The data were obtained from the 1000 Genomes project (see http://www.1000genomes.org/).

References

McVean et al, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature 491, 56-65 doi:10.1038/nature11632

Examples

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data(LCT)
x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)
x
which(x@snps$id == "rs4988235")


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